rs1819097

Variant names:

• chr21-10464180-C-A
• rs1819097
• ENST00000470054.5:n.660-682C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000470054.5(ENSG00000290523):​n.660-682C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.052 (0 hom., cov: 205)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000290523 ENST00000470054.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 2 publications found

Genes affected

ENSG00000290523 (HGNC:):

BAGE2 (HGNC:15723): (BAGE family member 2 (pseudogene)) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAGE2	NR_169269.1	n.695-682C>A		intron_variant	Intron 4 of 12
BAGE2	NR_169270.1	n.695-682C>A		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290523	ENST00000470054.5	n.660-682C>A		intron_variant	Intron 4 of 9	1
BAGE2	ENST00000496773.1	n.336-682C>A		intron_variant	Intron 2 of 14	6
ENSG00000290523	ENST00000807240.1	n.693-682C>A		intron_variant	Intron 4 of 10

Frequencies

GnomAD3 genomes AF: 0.0515 AC: 5074 AN: 98454 Hom.: 0 Cov.: 205

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0180

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0236

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0400

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0516 AC: 5079 AN: 98508 Hom.: 0 Cov.: 205 AF XY: 0.0523 AC XY: 2507 AN XY: 47956

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.122 AC: 2645 AN: 21724

American (AMR) AF: 0.0310 AC: 331 AN: 10662

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 122 AN: 2288

East Asian (EAS) AF: 0.0575 AC: 169 AN: 2940

South Asian (SAS) AF: 0.0770 AC: 214 AN: 2780

European-Finnish (FIN) AF: 0.0358 AC: 244 AN: 6810

Middle Eastern (MID) AF: 0.0258 AC: 5 AN: 194

European-Non Finnish (NFE) AF: 0.0261 AC: 1279 AN: 49010

Other (OTH) AF: 0.0414 AC: 57 AN: 1376

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0888 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.60
PhyloP100		-0.11

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1819097; hg19: chr21-11048277;